Cladistics does not resolve hobbit controversy

Homo floresiensis (nicknamed "the hobbit") is the name given to a hominin species whose remains were discovered in 2004 on the island of Flores, Indonesia. But do the bones represent a new species at all, or were they, mundanely, anatomically modern humans with some pathological disorder that caused them to have smaller brains (~400 cc) and be shorter (106 cm) than humans (~1130 cc and 147 cm, average for women and Indonesian women, respectively)?

I have previously made clear where I stand in that debate, and for what reasons, but at the same time I do have some reservations with a paper in the Journal of Human Evolution that applies cladistic analysis (also known as phylogenetics) to determine where in hominin evolution H. floresiensis fits in.

The authors, Argue et al., examined multiple morphological features of bones of H. floresiensis, H. ergaster, H. erectus, H. habilis, H. rudolfensis, A. africanus, A. afarensis, H. rhodesiensis, H. georgicus, and H. sapiens in order to compare them and construct cladograms (evolutionary or phylogenetic trees showing ancestral relationships). Because some scientists suggest that the smaller brain case could have been caused by microencephaly, they excluded cranial capacity from the comparisons.

The result is that two trees are the most parsimonious, meaning that they are the shortest of all the trees they examined. In other words, under the assumption that the fewer morphological changes between the species is the better model for the evolutionary relationship, these two trees are the most likely of all.

The two most parsimonious cladograms, with H. floresiensis branching off just after and just before H. habilis, respectively. Dmanisi is also known as Homo georgicus.

So the conclusion the authors make seems fair enough: H. floresiensis branched off either just after or just before H. habilis.

Skipping over the problems I have with the assumption of parsimony, does anyone else notice something really fishy so far?

The fishy part is that in order to construct cladograms like the ones above, the authors assumed that H. floresiensis and H. sapiens are different species. Once that is done, no other conclusion can be reached. It is perhaps interesting by itself to see what the evolutionary relationship is between them, assuming that they have one, but it can't address the question of whether they are different species or not. However, Argue et al. state clearly in their introduction that this is their goal:

Alternative interpretations include the possibility that the Liang Bua fossils represent a new hominin species, H. floresiensis (...), and that the holotype specimen, LB1, was a modern human, possibly afflicted with a pathological condition (...). These conflicting hypotheses are based on comparative analyses of the morphology of the bones with both archaic and modern Homo, typically using statistical methods to compare the Liang Bua bones with those of other hominins. The morphological and morphometric analyses have contributed much to the debate about H. floresiensis, but have not conclusively resolved the controversy about the position of the species in human evolution. We, therefore, use a different tool, cladistic analysis, which has not yet been applied to resolving this problem.

Again, I do not see how using cladistic analysis can be used to resolve this question of whether H. floresiensis was a human with a pathological condition or a separate species. In fact, the same issue exists between H. georgicus (Dmanisi) and H. erectus. H. georgicus is now thought to represent an early stage before H. erectus, rather than being a separate species. Yet, here they are assumed to be different species.

From their conclusion:

Based on rigorous cladistic analyses, we propose that H. floresiensis evolved in the Late Pliocene or Early Pleistocene. The first of our two equally parsimonious trees suggests that H. floresiensis branched after H. rudolfensis (represented by KNM-ER 1470) but prior to the divergence of H. habilis (represented by KNM-ER 1813 and OH 24). Alternatively, our results are equally supportive of H. floresiensis branching after the emergence of H. habilis.

Agreed. I too believe H. floresiensis to be a new species, and given that, I can accept the cladistic analysis (again, ignoring my issues with parsimony in cladistics).

In their earlier paper (Argue et al., 2006) the morphological data were used to support this conclusion, but, again, the results in the present paper does not "sustain H. floresiensis as a new species (...) and favor the hypothesis that H. floresiensis descended from an early species of Homo," when it is assumed that they are separate species.

6 comments:

The fishy part is that in order to construct cladograms like the ones above, the authors assumed that H. floresiensis and H. sapiens are different species. Once that is done, no other conclusion can be reached.

I don't think this is the case. The authors assumed that H. floresiensis and their sampled H. sapiens population(s) can be treated as separate taxa, but made no assumption about whether they're different species. After all, cladistics is fine with taxa below the species level.

Now it's true that an analysis like this couldn't confirm that H. sapiens and H. floresiensis were the same species, but it can certainly refute that claim. If they are the same species, then they should fall out as sister taxa on the trees. If they're different but very closely related species, then they should also fall out as sister taxa--that's why the trees couldn't unambiguously confirm the former case. But if they consistently don't fall out as sister taxa--which seems to be the case in this analysis--then they must be different and somewhat distantly-related species. (Assuming the parsimony method actually works and all.)

There's only one possibility explicitly ruled out by the way the authors set up their analysis: namely, that H. floresiensis falls within the subclade of H. sapiens represented by their sample of eleven humans. And even if that were the case, I suspect their analysis would still return the two groups as sisters, that being the closest result it could actually produce.

But if they want to doublecheck that, I suppose they should redo the analysis while scoring each human skeleton separately.

Now it's true that an analysis like this couldn't confirm that H. sapiens and H. floresiensis were the same species, but it can certainly refute that claim.

Recall that the opposing view is that the H. floresiensis phenotype is caused by disease, and if we were to accept that, then the cladistics don't refute that they are the same. If they had a disease that affected their morphology in many skeletal traits, then it would not be surprising that the analysis didn't group them with humans.

Again, my quip with this paper is really only how the authors phrase their conclusion. Assuming that the morphological differences aren't pathological, I find the cladistic analysis interesting (with reservations about parsimony).

Recall that the opposing view is that the H. floresiensis phenotype is caused by disease, and if we were to accept that, then the cladistics don't refute that they are the same.

It depends on the thoroughness of the analysis, I think. Given enough points of comparison, it could be established as highly unlikely that a disease was responsible for all of the characters placing H. floresiensis at some distance from H. sapiens.

Is this analysis sufficiently thorough? I don't have the expertise to venture an opinion. You raise an interesting issue, though--could we look at the characters responsible for floresiensis' position in these trees, and come up with a particular disease or disorder that would account for most of them? The backers of the "hobbits are diseased humans" hypothesis have already listed sets of traits that microcephaly would account for, of course, but AFAIK they haven't done so for a specific set of traits in conjunction with a cladistic phylogeny like this. That might help them narrow down the range of disorders that could be responsible.

If they had a disease that affected their morphology in many skeletal traits, then it would not be surprising that the analysis didn't group them with humans.

Only if that disease happened to affect those many traits in the exact way necessary to "fake" an affinity with another part of the tree, no? If the disease just made them weird, that would not (on average) cause them to be grouped elsewhere. Cladistics ignores unique apomorphies, and they'd still be closer to H. sapiens than to anything else.

And if the disease messed with so many of their characters so badly that they lost all (skeletal) trace of affinity to H. sapiens, is it likely that they'd be relatively well-localized on the optimal trees at all?

I guess the best way to answer it would be to add H. sapiens skeletons with microcephaly, Laron syndrome, etc. to the analysis, and see if they all cluster together but the floresiensis material still shows up elsewhere.

Is this analysis sufficiently thorough? I don't have the expertise to venture an opinion. You raise an interesting issue, though--could we look at the characters responsible for floresiensis' position in these trees, and come up with a particular disease or disorder that would account for most of them? The backers of the "hobbits are diseased humans" hypothesis have already listed sets of traits that microcephaly would account for, of course, but AFAIK they haven't done so for a specific set of traits in conjunction with a cladistic phylogeny like this. That might help them narrow down the range of disorders that could be responsible.

That would be interesting indeed.

Only if that disease happened to affect those many traits in the exact way necessary to "fake" an affinity with another part of the tree, no?

I think that if you take a bunch of traits and "randomize" some of them, then you would expect the taxon to move away from its original position, and then necessarily be placed somewhere else. Cladistics forces one affinity at a time (per tree).

I think it has been thoroughly demonstrated that the traits are not of any known disease, and I think that's enough to settle the issue until more evidence appears.

For another post, and a day spare with nothing else to do, I will be interested to read your reservations with parsinomy in cladistics. A method you seem to hate given that you let us know you have reservations on every other paragraph.

Pleiotropy comes from the Greek πλείων pleion, meaning "more", and τρέπειν trepein, meaning "to turn, to convert". It designates the occurrence of a single gene affecting multiple traits, and is a hugely important concept in evolutionary biology.

I'm a postdoc at UC Santa Barbara.

All Many aspects of evolution interest me, but my research focus is currently on microbial evolution, adaptive radiation, speciation, fitness landscapes, epistasis, and the influence of genetic architecture on adaptation and speciation.